FAQ Misc

This is a page for miscellaneous FAQs often asked of Jose.

Computing FAQs

How do I edit a page in this Wiki?

This is very easy. Just go to this test page

Then log in (top right corner) and the click the edit tab or the edit buttons to the right. Enter some text and click "preview" or "save" and it'll be there.

We use the Wiki because it makes posting info on the web extremely easy.

For more detailed help, there is always a link on the left of every wiki page that says "Help", which takes you to the MediaWiki help page

We use the "MediaWiki" software to run the Wiki, so that help is what's relevant. Note that Wikipedia also uses MediaWiki, so once you learn, you can create an entry for something you are interested on in Wikipedia!

How do I create an email list using Google Groups?

After trying various tools, we have found that the email lists provided by Google Groups are a very good solution. They are free, they have an easy web interface to subscribe and unsubscribe, they keep an archive of all the messages sent to the list, and can be customized with various levels of access.

To create an email list with Google Groups, follow these steps:

• You need an Google Account (preferable associated with a Gmail email address). If you don't have one, you need to create one first.
• Go to http://groups.google.com/
• After you login, click "Create a Group"
• Choose a simple name, and the access level. For most of our work, we use "restricted" lists.
• On the "Add Members" page, click "Add Members Directly", and enter the email addresses of the members and a welcome message. This is better than "inviting" the members as you avoid bothering people and associated delays. However Google is cautious to avoid that people set up lists for spam purposes, so they may not let you add everyone at once. Just add them in a few times over a day or so, if needed.
• Click on "Group Settings" on the right, and then on the tab "Email Delivery". A few important settings are there:
  • Set the "Subject Prefix" to e.g. "[test:%d]", where in this case "test" is the name of the group.
  • Under "Message Footer", activate the "Default Footer." If needed, you can then change to "Custom Footer" and edit further, e.g. by adding a link to the webpage for this particular project.
  • Under "Replies to Messages" change to "Replies are sent to the author of the message"
• In some cases, you may want to allow anyone to send emails to the list. This can be activated on the "Access" Tab, under "Who can post messages?", by choosing "Anyone can post".

How can I do conference calls and/or share screens?

• A free conference line can be obtained from http://www.freeconferencecall.com. We have used it a lot recently (2011) and it worked great. Everyone dials a long distance call to the conference number, so it is not toll free, but that's not really an issue anymore, as long distance calls are pretty cheap these days.

• For screen sharing you can use http://www.freescreensharing.com which we have also used, and works very well as long as everyone's internet is decent (which is needed for all such services) and it is free. If you sign up for this one, you automatically get a free conference call number as well.

Writing and Presenting FAQs

Do you have tips for writing papers?

• A must read: Whitesides Group: How to Write a Paper, Advanced Materials, 16(15), 1375 - 1377, 2004.
• A funny list of things one should not do in papers: Skillful Writing of an Awful Research Paper by Royce Murray
• Gopen and Swan on the Science of Scientific Writing, American Scientist, 1990

Do you have any tips on writing proposals?

• A usual diagram of the proposal structure
• A short useful series of tips for writing proposals
• A very good presentation from Waleed Abdatati of CU on proposal-writing (Group Password)

Do you have any tips for presentations?

• A useful article for beginning speakers
• Some useful tips for Group Meeting presentations

Peer-Reviewing FAQs

I am interested in reviewing papers (or proposals), how do I get started?

• You should read this article in Nature with advice to new reviewers
• You can mention this to your advisor or other experienced scientists in the field. When they get requests to review and don't have time for them (which is very common), they can suggest you as an alternative reviewer. You can also let editors of relevant journals know that you are interested in reviewing, sending them an email stating your interest, along with the topics you are qualified to review and your CV.
• For proposals you need to write to the program managers of the different funding agencies
• Journal Editors and Program Managers complain a lot of how hard it is to get people to agree to provide reviews, so if you do a good job in the first few, you will quickly have more papers to review and than time!

How do I respond to the reviews of a paper?

A shortcut to this item is http://tinyurl.com/resp-rev. This is written as a guide for people in our group working on one of their first papers, although it may be of use to others.

In terms of procedure:

• As soon as you get the reviews, please forward them to all coauthors, and ask for any input they may have. This gives them more time and saves a lot of time, if they care strongly about how we respond to some review comment.
• Then you should work on the revised paper and response document as discussed below
• The revised paper and response document needs to be shared with all coauthors before re-submission. It would be unethical to not share the response document with coauthors, even if the reviews were good and the changes are small. Depending on how extensive the reviews and revisions were and of how many coauthors we have, we may give between a few days and 2 weeks to the coauthors to get back to us. We need to hear from coauthors that they agree to re-submission before we can proceed.

Generally we need to submit three documents in response to the reviews:

• (1) A revised paper
• (2) A "difference version" of the revised paper, highlighting (e.g. with track changes in Word) all the changes between the submitted and revised versions.
  • For ACPD or AMTD paper, please take care to incorporate all the changes that may have been made at the proof stage (those should NOT be highlighted).
• (3) A point-by-point reply to all of the reviewer comments.
  • In this document we first copy all the reviewer comments, and number them as R1.1, (reviewer #1, comment #1), R1.2 and so on, in black text.
  • Then we reply below each one, in blue text, as A1.1 (reply to comment #1 of reviewer #1), A1.2, and so on.
  • All changes to the document text need to be given in quotes and in bold in this document.

Some items to take into account when preparing responses:

• It is good to first create a response document and propose responses to each question, and then share the proposed responses with the key coauthors, before making all the changes in the manuscript. Otherwise time can be wasted by having to change 2 documents several times, before we decide on the final responses.
• You can read many examples of responses to reviews in the discussion section of ACP and AMT papers.
  • However, note that some of the responses are of mediocre quality. We strive for high-quality work, thus it is not OK to copy all practices you may see on those responses.
• Some good examples of good response documents include:
  • This response document of Marr et al., ACPD 2006.
  • The responses in Aiken et al., ACPD 2010.
  • (If you see other very well crafted examples, pls link them here or let us know)
• We do not need to implement all the changes requested by the reviewers. Sometimes the reviewers are reading the paper quickly or don't have much background in some sub-area, and thus some comments may reflect a misunderstanding of the manuscript. In these cases it is OK to to disagree with the reviewer, although it is good to ask ourselves: "Could the misunderstanding be caused by our manuscript being unclear? Could the manuscript be made clearer to avoid similar misunderstandings by readers?"

If the paper goes to further rounds of review in ACPD or AMTD

• In these journals the reviews and responses to the first round of reviews are public, but later rounds are not. Changing this procedure to make later rounds public has been discussed at the Editors meetings of these journals, but for the time being things will stay as is.
• However the Editorial Board encourages authors or editors to add a final comment to the paper, posting the reviews and responses to further rounds of review, after EVERYONE involved (authors, editor, and referees) have agreed to such public posting. An example of a final comment along these lines is in the public discussion of this paper.

Scientific Literature FAQs

Why does your group publish so much on ACP?

ACP has several key advantages over traditional journals:

• Free open access to papers
• Papers are public BEFORE they are reviewed. In "secret review" journals, nobody knows that the paper even exists until it has been accepted and appears on the web. That represents a delay of typically 4-8 months, sometimes more than a year, in the paper being public, which hurts the visibility of the work and increases the probability of being scooped.
• The reviews and the author responses are public. This is advantageous for at least two reasons:
  • The reviews and responses are often very useful to learn quickly what is new, controversial, or well-established etc. about a paper
  • The transparency of the publication process is also increased.
• Non-reviewers can also publish short comments on any paper. This is very useful to receive input from other researchers in the community (even as it creates more work in responding to those extra comments).
• In ACP also the special issues are particularly easy, a web page is created for the issue and papers are posted there as they are accepted, and they are ongoing special issues where people can publish papers as the analysis proceeds. E.g. for the MILAGRO special issue papers were published over 2.5 years, and for the MCMA-2003 special issue they were published over 5 years. It was a great benefit, then and now, to have all the papers together there.
• For all of the above reasons, ACP has effectively become the prime journal in Atmospheric Chemistry, surpassing JGR and others in e.g. Impact Factor, Special Issues, etc.
• Much of this also applies to AMT (Atmospheric Measurement Techniques), a recent journal on the ACP system)

That said, it is always good to publish on a variety of journals as they reach different readerships etc.

How do you determine whether a paper is "Highly Cited" according to Thomson ISI

Thomson ISI publishes thresholds for papers in each field (e.g. Chemistry, Geosciences, or Mech Eng -- this depends on the classification of each journal into fields by ISI) and each year, above which a paper is highly cited. As of Oct-2010, the thresholds are posted in this page (although ISI often moves them around). Basically they rank the papers by the number of citations, and they report the number of citations that separates the 1% most cited from the 99% less cited. So e.g. every year we look up the list on the web, and then we compare the citations of our papers with the relevant thresholds for each year of publication and journal field. In our group publications page we highlight in bold all of those papers.

The categories for the journals most relevant to us are:

• Geosciences: JGR, GRL, ACP
• Environment/Ecology: ES&T
• Engineering: AS&T
• Chemistry: Anal. Chem.

Can you do a chemical analysis for me?

• We are a research group and generally don't do chemical analyses for others, as our techniques are very specialized for aerosols and generally are too complex for other samples. We can always discuss if you have an aerosolizable sample and there is a common research interest, or if the analysis would be quick.
• We don't have a gas or liquid chromatograph, or an electrospray instrument, or an ion chromatograph.
• If you want to run a mass spec analysis on an organic sample (e.g. GC-MS, electrospray), you should contact Dr. Shuji Kato of the CHEM/CIRES Central Analytical Facility
• If you need to do elemental analysis, you should contact the ICPMS Facility in CU Geology, operated by Prof. Tom Marchitto